
Continuity mistake: When Thade takes the weapon from Leo the weapon is a futuristic laser type gun. When Thade is firing the weapon after being locked in the command centre, the gun is a stainless steel Beretta brigadier model. (01:50:00)

Revealing mistake: After the trained chimp is shot and is crawling into the cage, they show a shot of an ape turning around. You don't even have to look hard to see it but there's a two inch strip all the way down his face with no makeup. Clear as day. (01:41:30)
Chosen answer: Tim Burton has been quoted MANY times as saying it isn't supposed to make sense. Best guess is Leo travelled not just into the future, but into another dimension as well. Ironically, this ending is far more true to Peirre Boulle's original ending than the first Apes movie.
Grumpy Scot